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PXD055510

PXD055510 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCysteine-directed isobaric labeling combined with GeLC-FAIMS MS for quantitative top-down proteomics
DescriptionThe quantification of proteoforms, i.e., all molecular forms in which proteins can be present, by top-down proteomics provides essential insights into biological processes at the molecular level. Isobaric labeling-based quantification strategies are suitable for multi-dimensional separation strategies and allow for multiplexing of the samples. Here, we investigated cysteine-directed isobaric labeling by iodoTMT in combination with a gel- and gas-phase fractionation (GeLC-FAIMS-MS) for in-depth quantitative proteoform analysis. We optimized the acquisition workflow (i.e., the FAIMS compensation voltages, isolation windows, acquisition strategy, and fragmentation method) using a two-proteome mix to increase the number of quantified proteoforms and reduce ratio compression. Additionally, we implemented a mass feature-based quantification strategy in the widely used deconvolution algorithm FLASHDeconv, which improves and facilitates data analysis. The optimized iodoTMT GeLC-FAIMS-MS workflow was applied to quantitatively analyze the proteome of Escherichia coli grown under glucose or acetate as the sole carbon source, resulting in the identification of 726 differentially abundant proteoforms.
HostingRepositoryPRIDE
AnnounceDate2025-05-07
AnnouncementXMLSubmission_2025-05-07_02:47:57.248.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAndreas Tholey
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListcysTMT6plex reporter+balance reagent cysteine disulfide
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-09-03 04:19:34ID requested
12025-05-07 02:47:58announced
Publication List
10.1021/acs.jproteome.4c00835;
Matzanke T, Kaulich PT, Jeong K, Takemori A, Takemori N, Kohlbacher O, Tholey A, Cysteine-Directed Isobaric Labeling Combined with GeLC-FAIMS-MS for Quantitative Top-Down Proteomics. J Proteome Res, 24(3):1470-1480(2025) [pubmed]
Keyword List
submitter keyword: Top-down proteomics
TMT labeling
quantitative proteomics
FAIMS
GeLC
PEPPI
Contact List
Andreas Tholey
contact affiliationSystematic Proteome Research & Bioanalytics, Institute for Experimental Medicine Christian-Albrechts-Universität zu Kiel 24105 Kiel, Germany
contact emaila.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliationSystematic Proteome Research & Bioanalytics, University of Kiel
contact emaila.tholey@iem.uni-kiel.de
dataset submitter
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